BIOPHYSICAL THEORY AND MODELING |
Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA
Taner Z Sen 1*, Margaret Kloster 2, Robert L Jernigan 1, Andrzej Kolinski 3, Janusz M Bujnicki 4 and Andrzej Kloczkowski 1
1 Iowa State University
2 University of Washington
3 University of Warsaw
4 Adam Mickiewicz University
* To whom correspondence should be addressed. E-mail: taner{at}iastate.edu.
Submitted on June 22, 2007
Revised on July 26, 2007
Accepted on 5 November 2007
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Abstract |
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E. coli requires an efficient transport and signaling system to successfully sequester iron from its environment. FecA, a TonB-dependent protein, serves a critical role in this processes: first, it binds and transports iron in the form of ferric citrate, and second, it initiates a signaling cascade which results in the transcription of several iron transporter genes in interaction with inner membrane proteins. The structure of the plug and barrel domains and the periplasmic N-terminal domain (NTD) are separately available. However, the linker connecting the plug and barrel and the NTD domains is highly mobile, which prevents determining the FecA structure as a whole assembly. Here, we reduce the conformation space of this linker into most probable structural models using the modeling tool CABS, then apply normal mode analysis to investigate the motions of the whole structure of FecA by using elastic network models. We relate the FecA domain motions to the outer-inner membrane communication, which initiates transcription. We observe that the global motions of FecA assign flexibility to the TonB-box and the NTD, and control the exposure of TonB-box for binding to the TonB inner membrane protein, suggesting how these motions relate to FecA function.
Key Words:
CASP, ab initio, elastic network models, folding, membrane proteins, structure prediction
